[webmaven]

> I wonder whether its possible to transplant the bacteria out before such a treatment and introduce them again later..

In theory yes, but there is the challenge of avoiding re-infection with the one species you're being treated to eliminate.

[Demigod33]

Is the gut usually the main target or just as byproduct getting wiped? If not then its not necessarily an issue.

[webmaven]

The target species may not be thriving in your gut, if the location of the infection you're treating is elsewhere, but it is probably present.